fixed call to sub pipeline

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -231,7 +231,7 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
     if (filename.endsWith(".gzip")) filename = filename.substring(0,filename.size - 5)
     if (filename.endsWith(".fastq")) filename = filename.substring(0,filename.size - 6)
     //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
-    fastqcCommand.output = outDir + "/" + filename + "_fastqc.ouput"
+    fastqcCommand.output = outDir + "/" + filename + "_fastqc.output"
     fastqcCommand.afterGraph
     add(fastqcCommand)
     return fastqcCommand

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -109,7 +109,8 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
       flexiprep.input_R1 = fastq_R1
       if (paired) flexiprep.input_R2 = fastq_R2
       flexiprep.outputDir = outputDir + "flexiprep/"
-      flexiprep.script
+      flexiprep.init
+      flexiprep.biopetScript
       addAll(flexiprep.functions) // Add function of flexiprep to curent function pool
       fastq_R1 = flexiprep.outputFiles("output_R1")
       if (paired) fastq_R2 = flexiprep.outputFiles("output_R2")